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Talkin’ ’bout my generation
April 2011
by David Hutton  |  Email the author


REDWOOD CITY, Calif.—With an eye on next-generation sequencing (NGS) analysis, Ingenuity Systems has entered into a research collaboration with Covance. The companies will work together to develop new and novel approaches using Ingenuity's IPA software to obtain more actionable insights from NGS data and to answer research questions in a relevant biological context.
"We're delighted that Covance has selected IPA for its NGS workflows," says Doug Bassett, chief scientific and technology officer at Ingenuity Systems. "We've been involved in several NGS collaborations recently, and our partnership with Covance, a leading drug development services company, represents another powerful validation of IPA's value in the NGS space. It is exciting to see IPA being used to accelerate and inform so much groundbreaking research."
Thomas Turi, vice president of science and technology for Covance Discovery and Translational Services, notes that this is the first formal collaboration between the Covance Genomics Laboratory (CGL) and Ingenuity Systems.
"Prior to its acquisition by Covance, CGL (formerly known as Rosetta Inpharmatics) was a significant user of Ingenuity's IPA software," he says. "Additionally, there had previously been significant interactions between key scientific leaders at Covance and Ingenuity that facilitated this collaboration."
Ingenuity Systems is a provider of information solutions and custom services for life-science researchers, computational biologists and bioinformaticists and life science industry suppliers.
According to Bassett, Covance proved to be a good fit for this effort because of the company's standing as a provider of genomics solutions for the drug discovery and development industry and the fact that the companies share many of the same customers. 
"Covance is also similarly forward-looking in how they are thinking about next-generation sequencing technologies," he says. "Both of our companies recognize that without biological interpretation, the value and potential in NGS technologies will not be unlocked for our mutual customers. Having Excel files of data or a list of variants or genes with associated statistics is a first step, but it does not get researchers to their end goal of answering a scientific question." 
The collaboration, Turi points out, is aimed at providing deeper insights and interpretation of biological pathways and networks from genomic data.
"The key part of this collaboration is aimed specifically at making sense of large volumes of next-generation sequencing data to provide a systematic and multi-dimensional view of human genetics and cover various data types, e.g., gene expression, genotyping, splice variation and methylation," he says. "Integrating these various data types into coherent biological stories is what constitutes the most challenging step."
In the collaboration, Ingenuity and Covance are working together to develop new methodologies to help pharmaceutical clients maximize the value of their NGS investments and obtain more actionable insights from NGS data, including isoform-level biological interpretation for RNA-Seq studies leveraging Ingenuity knowledgebase content, and helping customers using resequencing technology to get from a list of 3 million-plus variants down to the less than 50 most compelling for follow-up.
"Ingenuity's Knowledge Base of expert-curated, structured biomedical content provides the biological context necessary to move past long lists of genes, isoforms and variants, enabling researchers to more quickly uncover those that are most critical to biology," Bassett notes. "Using this approach, Covance can more rapidly and confidently narrow in on what is interesting or unique in a dataset and deliver more meaningful results to their customers."
Moreover, Bassett says the companies share a common conviction that analyzing data in the context of known biology—like pathways, processes and diseases—is essential to uncovering novel insights and helping researchers quickly get to high-value outcomes like causal disease variants, biomarker identification, target ID and validation, understanding drug mechanism of action and safety assessment.
According to Bassett, success of this collaboration can be measured by the effectiveness and efficiency of their mutual customers.
"This partnership should enable scientists to invest their valuable time on the biological interpretation of their data—validating hypotheses, assessing safety, prioritizing biomarkers, identifying causal variants and so on—not dealing with data processing issues, manually iterating through large lists of variants or genes, or struggling to place their data into the context of previously published mutations and findings," he points out.
Being digital in nature and due to its larger dynamic range compared to microarrays, this technology helps in the identification of novel genetic alterations, non- coding RNAs and alternative splicing, in addition to gene expression associated with various diseases.
"As more data becomes available, there is a growing need in the industry to develop automated pipelines to integrate and mine complex datasets for better understanding of biological processes that impact drug development," Turi explains. "Covance plans to use this collaboration to further develop its pipeline for analyzing complex datasets and aid pharmaceutical and biotech partners to identify targets or biomarkers for their drug discovery programs. Covance will test these capabilities using a pilot project with Institute of Systems Biology (ISB) targeting glioblastoma."
Additionally, Turi says the collaboration will further enhance Covance's offerings in the genomics arena. "As next-generation sequencing rapidly becomes the focus of genomics, Covance realizes that in the near future the platforms will significantly shift into the space of next-generation sequencing," he says.
Code: E041111



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